The effects of four rates of application of fertilizer, with cow manure (3000 kg ha1), urea (100 (kg ha1) and triple super phosphate (TSP) (100 kg ha1) (treatment F)), treatment F 0.5 (treatment 0.5F), treatment F 1.5 (treatment 1.5F) and treatment F 2 (treatment 2F), on periphyton, plankton and water quality in tropical freshwater ponds were studied. The highest periphyton biomass in terms of dry matter (3.27 mg cm2 substrate), ash-free dry matter (2.06 mg cm2 substrate) and chlorophyll a (7.49 ?g cm2 substrate) developed in treatment 1.5F. The ash content of periphyton was lower in treatment 1.5F (38␘f dry matter) than in other treatments (57-66␘f dry matter). Total ammonia and chlorophyll a of water increased with fertilization rate. Treatment 1.5F (cow manure, urea and TSP at rates of 4500, 150 and 150 kg ha1 respectively) appears to be the optimum, yielding high quantity and quality periphyton. By supplying a substrate area for periphyton equivalent to the pond surface, it was estimated that this level of fertilization could support a fish production of around 5000 kg ha1 y1, without recourse to supplementary food.